[BioC] Hostname bug?

[Seth Falcon]

Hi Mark,

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
> I can update packages from the Windows menu of R 2.3.1, but not from R
> 2.4. I get the following error message:
>
> Warning: unable to access index for repository
> http://www.bioconductor.org/bin/windows/contrib/2.4
>
> sessionInfo()
>
> R version 2.4.0 Under development (unstable) (2006-08-29 r39012) 
> i386-pc-mingw32 
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"  "base"     

Thanks for the report.  We have not added the BioC 1.9 repository to
the location that the Windows R GUI searches and hence the warning
message (and failure to update).

At present, I suspect that even in R 2.3.z, this doesn't work as
desired because the operation only searches one of Bioconductor's
repositories.  As a result, various dependencies will not be updated.

We will look into addressing both of these issues for R 2.4 and the
upcoming BioC release.

For now, I would recommend the following to update your packages
(should work for R 2.4 series):

library("Biobase")
update.packages(repos=biocReposList(), dependencies=TRUE)

Bw,

+ seth